Sequencing, assembly, and annotation of mitogenomes

Specimens were individually sequenced using the Ion Torrent™ S5™ platform (ThermoFisher Scientific, Waltham, MA, USA) available at the Central Analytical Facilities of Stellenbosch University, South Africa. Sequence libraries were prepared using the Ion Xpress™ Plus gDNA Fragment Library Kit (ThermoFisher Scientific, Waltham, MA, USA), according to the protocol MAN0009847, REV J.0. Libraries were pooled and sequenced using the Ion 540™ Chef Kit (ThermoFisher Scientific, Waltham, MA, USA). The Ion Torrent reads were quality trimmed with a 30-base sliding-window at an average threshold of Q16. The remaining sequencing reads were then filtered for read length, where any reads shorter than 25 bases were removed from the data. Reference-based assembly of the next-generation sequencing (NGS) reads was performed using mitogenomes of the closest Saturniidae relatives available on GenBank (Table S1). NGS reads were assembled and mapped to the reference sequences on Geneious Prime v2021.1.1 (https://www.geneious.com/) using the “Map to reference” function, under the low to medium sensitivity option and fine-tuning up to five iterations. The open reading frames of the expected 13 mitochondrial protein-coding genes (PCGs) were identified with Geneious Prime using the invertebrate mitochondrial genetic code. Transfer RNA (tRNA) genes were located with ARWEN software (http://130.235.244.92/ARWEN/) (Laslett & Canbäck, 2008), under the default composite metazoan mitochondrial genetic code. The two ribosomal RNA (rRNA) genes and the non-coding AT-rich region were annotated by manual comparison to other Saturniidae mitogenomes available on GenBank. The raw sequence data were deposited on GenBank (PRJNA796275), as well as the 12 assembled and annotated mitogenomes ({"type":"entrez-nucleotide","attrs":{"text":"OL912807","term_id":"2198384007","term_text":"OL912807"}}OL912807 to {"type":"entrez-nucleotide","attrs":{"text":"OL912817","term_id":"2198384198","term_text":"OL912817"}}OL912817/ and {"type":"entrez-nucleotide","attrs":{"text":"OL912953","term_id":"2198384216","term_text":"OL912953"}}OL912953).